Ultrasonic fatigue testing is quite a useful tool for exploring the high-cycle and very-high-cycle fatigue properties of materials. Damping monitoring has been proved to be fairly effective in indicating the generated defects or damage in the testing specimen. In this work, two damping monitoring methods are comparatively studied, i.e., our recently proposed quantitative electromechanical impedance method and the traditional vibration-free decay method. Industrial pure copper and 6061 aluminum alloy are used for fatigue testing and damping monitoring. To exclude the differences of temperature effect on the testing system, the same duty ratio of 15.4% is employed in the ultrasonic fatigue testing. The results show that both methods can effectively monitor the system damping during testing and the damping evolution process just before failure. Specifically, the free decay method can obtain more damping data and has advantages in monitoring metals, such as aluminum alloys, whose fracture process is very quick. However, the system damping obtained by free decay is strongly dependent on the testing stresses and signal processing and is thus not suitable for failure prediction of specimens. In comparison, the system damping obtained by using the quantitative electromechanical impedance method is independent of the testing stresses. Thus, a definite relationship between the system damping and specimen’s internal friction can be established. However, tens of seconds are required for accurate damping measurement using the quantitative electromechanical impedance method, leading to a low duty ratio of the ultrasonic fatigue testing. In practical, both the methods are suggested for monitoring of early damage during ultrasonic fatigue testing.